Variant Calling

Service Description

Alignment and variant calling, which can include single-nucleotide variants (SNVs), copy number variants (CNVs), and structural variants (SVs).

Required Input Files:

• Fastq.gz files
• Organism (Human or Mouse).
• Normal controls - if doing comparative analysis

Pipeline Tools:

• BWA-MEM v0.7.15
• FastQC
• GATK4.1.8.0
• Picard
• Strelka2
• MuSE
• [VariantNormalize]
• VEPv110
• VCF2MAF
• CNVkit
• LUMPY
• SvABA
• Manta
• AnnotSV

Primary Output Files:

• VCF/MAF files
• Deduped sorted aligned .bam/bai files
• Picard Metrics
• CNV plots
• Structural Variant Analysis
• Summary Reports